Twenty years of artificial directional selection have shaped the genome of the Italian Large White pig breed

Abstract

In this study, we investigated at the genome-wide level if 20 years of artificial directional selection based on boar genetic evaluation obtained with a classical BLUP animal model shaped the genome of the Italian Large White pig breed. The most influential boars of this breed (n = 192), born from 1992 (the beginning of the selection program of this breed) to 2012, with an estimated breeding value reliability of >0.85, were genotyped with the Illumina Porcine SNP60 BeadChip. After grouping the boars in eight classes according to their year of birth, filtered single nucleotide polymorphisms (SNPs) were used to evaluate the effects of time on genotype frequency changes using multinomial logistic regression models. Of these markers, 493 had a PBonferroni < 0.10. However, there was an increasing number of SNPs with a decreasing level of allele frequency changes over time, representing a continuous profile across the genome. The largest proportion of the 493 SNPs was on porcine chromosome (SSC) 7, SSC2, SSC8 and SSC18 for a total of 204 haploblocks. Functional annotations of genomic regions, including the 493 shifted SNPs, reported a few Gene Ontology terms that might underly the biological processes that contributed to increase performances of the pigs over the 20 years of the selection program. The obtained results indicated that the genome of the Italian Large White pigs was shaped by a directional selection program derived by the application of methodologies assuming the infinitesimal model that captured a continuous trend of allele frequency changes in the boar population.

Genome-wide association study for ham weight loss at first salting in Italian Large White pigs: towards the genetic dissection of a key trait for dry-cured ham production

“…It also could be possible that, as ham weight loss at first salting has been one of the most relevant selection objectives over the last two decades in this population, major positive QTL alleles might be already fixed or almost fixed (Schiavo et al . ), explaining, on the other hand, the presence of many minor QTL still segregating and the absence of highly significant SNPs, as reported in this GWAS.…”

Whole-genome sequencing of European autochthonous and commercial pig breeds allows the detection of signatures of selection for adaptation of genetic resources to different breeding and production systems

“…Commercial pig breeds (Italian Large White, Italian Duroc and Italian Landrace) that have been under intensive selection programmes since the beginning of the 1990' [95][96][97] were compared with local pig breeds. Signals were detected on seven chromosomes: SSC1, 5, 9, 10, 11, 13 and 15 (see Additional file 1: Table S14 and Additional file 2: Figure S7).…”

Identification of a potential functional single nucleotide polymorphism for fatness and growth traits in the 3′-untranslated region of the PCSK1 gene in chickens1

“…The SNP c.*900G > A was genotyped by the PCR-RFLP method. The primers (5′ GGT TTA GAC TAG TGA CAG TCA TAT TC 3′ and 5′ CCT TCC CTC TAT TTA TGA CTC TC 3′) were designed to amplify a 565-bp fragment containing the SNP c.*900G > A using Primer Premier 5 software (PREMIER Biosoft International, Palo Alto, CA) (Schiavo et al, 2016). This model assumes a linear relationship between time (generation) and a log transformation of the ratio between allele frequencies.…”